Multiple sequence alignment - TraesCS5D01G156500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G156500 chr5D 100.000 5622 0 0 1 5622 244629632 244624011 0.000000e+00 10382.0
1 TraesCS5D01G156500 chr5D 91.262 103 6 1 5360 5462 250069717 250069618 2.730000e-28 137.0
2 TraesCS5D01G156500 chr5B 94.531 2633 80 16 3018 5622 278014300 278011704 0.000000e+00 4006.0
3 TraesCS5D01G156500 chr5B 90.024 1684 56 42 112 1745 278018445 278016824 0.000000e+00 2076.0
4 TraesCS5D01G156500 chr5B 92.381 840 51 6 1806 2644 278016733 278015906 0.000000e+00 1184.0
5 TraesCS5D01G156500 chr5B 92.201 359 18 5 2636 2987 278014989 278014634 3.020000e-137 499.0
6 TraesCS5D01G156500 chr5B 93.750 96 4 2 5361 5454 461134478 461134383 5.870000e-30 143.0
7 TraesCS5D01G156500 chr5A 89.510 3289 173 74 168 3377 328811872 328808677 0.000000e+00 4004.0
8 TraesCS5D01G156500 chr5A 97.218 1438 36 3 3372 4809 328808512 328807079 0.000000e+00 2431.0
9 TraesCS5D01G156500 chr5A 97.989 746 14 1 4878 5622 328805289 328804544 0.000000e+00 1293.0
10 TraesCS5D01G156500 chr5A 85.581 215 23 5 1461 1671 19541872 19541662 9.480000e-53 219.0
11 TraesCS5D01G156500 chr5A 91.346 104 8 1 5365 5467 698639725 698639622 2.110000e-29 141.0
12 TraesCS5D01G156500 chr5A 94.805 77 4 0 4806 4882 328805580 328805504 2.750000e-23 121.0
13 TraesCS5D01G156500 chr3D 77.536 1104 198 30 3548 4620 454746669 454747753 2.220000e-173 619.0
14 TraesCS5D01G156500 chr3D 85.514 214 31 0 1461 1674 454746189 454746402 2.040000e-54 224.0
15 TraesCS5D01G156500 chr3B 77.428 1112 185 37 3548 4620 597546074 597547158 2.240000e-168 603.0
16 TraesCS5D01G156500 chr3B 85.581 215 31 0 1461 1675 597545598 597545812 5.670000e-55 226.0
17 TraesCS5D01G156500 chr3A 77.248 1112 187 37 3548 4620 596794945 596796029 4.850000e-165 592.0
18 TraesCS5D01G156500 chr3A 85.581 215 31 0 1461 1675 596794463 596794677 5.670000e-55 226.0
19 TraesCS5D01G156500 chr4B 85.981 214 26 4 1461 1672 412107941 412107730 5.670000e-55 226.0
20 TraesCS5D01G156500 chr4D 85.514 214 27 4 1461 1672 334118573 334118362 2.640000e-53 220.0
21 TraesCS5D01G156500 chr4D 80.292 274 52 2 3576 3848 334117682 334117410 7.380000e-49 206.0
22 TraesCS5D01G156500 chr4A 85.514 214 27 4 1461 1672 139545394 139545605 2.640000e-53 220.0
23 TraesCS5D01G156500 chr4A 80.597 268 50 2 3576 3842 139546228 139546494 7.380000e-49 206.0
24 TraesCS5D01G156500 chr2D 92.929 99 6 1 5355 5452 15192977 15192879 5.870000e-30 143.0
25 TraesCS5D01G156500 chr6D 92.079 101 6 2 5349 5449 59623161 59623259 2.110000e-29 141.0
26 TraesCS5D01G156500 chr6D 75.385 195 44 3 4321 4513 452497514 452497322 2.160000e-14 91.6
27 TraesCS5D01G156500 chr2B 90.476 105 6 4 5356 5459 559179602 559179501 9.820000e-28 135.0
28 TraesCS5D01G156500 chr1A 87.826 115 11 2 5349 5463 427520483 427520594 1.270000e-26 132.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G156500 chr5D 244624011 244629632 5621 True 10382.00 10382 100.00000 1 5622 1 chr5D.!!$R1 5621
1 TraesCS5D01G156500 chr5B 278011704 278018445 6741 True 1941.25 4006 92.28425 112 5622 4 chr5B.!!$R2 5510
2 TraesCS5D01G156500 chr5A 328804544 328811872 7328 True 1962.25 4004 94.88050 168 5622 4 chr5A.!!$R3 5454
3 TraesCS5D01G156500 chr3D 454746189 454747753 1564 False 421.50 619 81.52500 1461 4620 2 chr3D.!!$F1 3159
4 TraesCS5D01G156500 chr3B 597545598 597547158 1560 False 414.50 603 81.50450 1461 4620 2 chr3B.!!$F1 3159
5 TraesCS5D01G156500 chr3A 596794463 596796029 1566 False 409.00 592 81.41450 1461 4620 2 chr3A.!!$F1 3159
6 TraesCS5D01G156500 chr4D 334117410 334118573 1163 True 213.00 220 82.90300 1461 3848 2 chr4D.!!$R1 2387
7 TraesCS5D01G156500 chr4A 139545394 139546494 1100 False 213.00 220 83.05550 1461 3842 2 chr4A.!!$F1 2381

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
967 1029 0.311790 ACACAAATCAAGCGCCAGTG 59.688 50.000 2.29 5.35 0.00 3.66 F
1140 1206 1.343465 TCGGTCTCTTCCCTTGTTGAC 59.657 52.381 0.00 0.00 0.00 3.18 F
1967 2122 0.033504 ATTGGCGTGTGTCGTCTTCT 59.966 50.000 0.00 0.00 45.15 2.85 F
3228 4648 0.107703 TGTGGTACAGCATGCTAGCC 60.108 55.000 22.19 21.34 41.80 3.93 F
3290 4715 0.830444 TGTGGAGTGGTACGCCTTCT 60.830 55.000 3.50 0.00 38.97 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1797 1952 0.258194 ACTCCCTCCGTTCCGAGTAT 59.742 55.000 0.00 0.00 33.87 2.12 R
1985 2140 1.373570 GTCCTTCATGCCACAGTAGC 58.626 55.000 0.00 0.00 0.00 3.58 R
3889 5889 1.740296 GGCCGTGTCATTGTACGCT 60.740 57.895 9.57 0.00 38.87 5.07 R
4448 6460 0.033796 ATGACAGCCCACCCATTCAG 60.034 55.000 0.00 0.00 0.00 3.02 R
4973 8717 1.069358 CTAGCCAAGTAGTAGCCAGGC 59.931 57.143 1.84 1.84 42.31 4.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 9.448438 TTTACATCACTAAGTATTTGCTGATGT 57.552 29.630 19.89 19.89 44.70 3.06
29 30 8.425577 ACATCACTAAGTATTTGCTGATGTAC 57.574 34.615 16.93 0.00 43.07 2.90
30 31 8.040727 ACATCACTAAGTATTTGCTGATGTACA 58.959 33.333 16.93 0.00 43.07 2.90
31 32 9.049523 CATCACTAAGTATTTGCTGATGTACAT 57.950 33.333 8.43 8.43 36.16 2.29
32 33 9.618890 ATCACTAAGTATTTGCTGATGTACATT 57.381 29.630 10.30 0.00 0.00 2.71
33 34 9.448438 TCACTAAGTATTTGCTGATGTACATTT 57.552 29.630 10.30 0.00 0.00 2.32
50 51 8.528917 TGTACATTTAGTAGTACAAGCAACAG 57.471 34.615 2.52 0.00 45.30 3.16
51 52 8.361889 TGTACATTTAGTAGTACAAGCAACAGA 58.638 33.333 2.52 0.00 45.30 3.41
52 53 9.199982 GTACATTTAGTAGTACAAGCAACAGAA 57.800 33.333 2.52 0.00 40.16 3.02
53 54 8.311650 ACATTTAGTAGTACAAGCAACAGAAG 57.688 34.615 2.52 0.00 0.00 2.85
54 55 8.148351 ACATTTAGTAGTACAAGCAACAGAAGA 58.852 33.333 2.52 0.00 0.00 2.87
55 56 8.988934 CATTTAGTAGTACAAGCAACAGAAGAA 58.011 33.333 2.52 0.00 0.00 2.52
56 57 7.941795 TTAGTAGTACAAGCAACAGAAGAAC 57.058 36.000 2.52 0.00 0.00 3.01
57 58 5.914033 AGTAGTACAAGCAACAGAAGAACA 58.086 37.500 2.52 0.00 0.00 3.18
58 59 5.753921 AGTAGTACAAGCAACAGAAGAACAC 59.246 40.000 2.52 0.00 0.00 3.32
59 60 3.877508 AGTACAAGCAACAGAAGAACACC 59.122 43.478 0.00 0.00 0.00 4.16
60 61 2.722094 ACAAGCAACAGAAGAACACCA 58.278 42.857 0.00 0.00 0.00 4.17
61 62 3.290710 ACAAGCAACAGAAGAACACCAT 58.709 40.909 0.00 0.00 0.00 3.55
62 63 3.316308 ACAAGCAACAGAAGAACACCATC 59.684 43.478 0.00 0.00 0.00 3.51
63 64 3.498774 AGCAACAGAAGAACACCATCT 57.501 42.857 0.00 0.00 0.00 2.90
64 65 4.623932 AGCAACAGAAGAACACCATCTA 57.376 40.909 0.00 0.00 0.00 1.98
65 66 4.573900 AGCAACAGAAGAACACCATCTAG 58.426 43.478 0.00 0.00 0.00 2.43
66 67 4.284490 AGCAACAGAAGAACACCATCTAGA 59.716 41.667 0.00 0.00 0.00 2.43
67 68 5.046014 AGCAACAGAAGAACACCATCTAGAT 60.046 40.000 0.00 0.00 0.00 1.98
68 69 5.064452 GCAACAGAAGAACACCATCTAGATG 59.936 44.000 23.53 23.53 38.51 2.90
69 70 6.169094 CAACAGAAGAACACCATCTAGATGT 58.831 40.000 27.03 14.87 37.11 3.06
70 71 7.323420 CAACAGAAGAACACCATCTAGATGTA 58.677 38.462 27.03 0.00 37.11 2.29
71 72 6.868622 ACAGAAGAACACCATCTAGATGTAC 58.131 40.000 27.03 14.75 37.11 2.90
72 73 6.437477 ACAGAAGAACACCATCTAGATGTACA 59.563 38.462 27.03 0.00 37.11 2.90
73 74 7.124901 ACAGAAGAACACCATCTAGATGTACAT 59.875 37.037 27.03 8.43 37.11 2.29
74 75 7.984050 CAGAAGAACACCATCTAGATGTACATT 59.016 37.037 27.03 16.87 37.11 2.71
75 76 8.543774 AGAAGAACACCATCTAGATGTACATTT 58.456 33.333 27.03 15.51 37.11 2.32
76 77 9.167311 GAAGAACACCATCTAGATGTACATTTT 57.833 33.333 27.03 15.93 37.11 1.82
77 78 9.520515 AAGAACACCATCTAGATGTACATTTTT 57.479 29.630 27.03 15.29 37.11 1.94
99 100 6.939132 TTTACCTAACAAACGGTGAATTCA 57.061 33.333 3.38 3.38 34.76 2.57
100 101 7.513371 TTTACCTAACAAACGGTGAATTCAT 57.487 32.000 12.12 0.00 34.76 2.57
101 102 8.618702 TTTACCTAACAAACGGTGAATTCATA 57.381 30.769 12.12 0.00 34.76 2.15
102 103 6.737254 ACCTAACAAACGGTGAATTCATAG 57.263 37.500 12.12 11.08 30.90 2.23
103 104 5.123344 ACCTAACAAACGGTGAATTCATAGC 59.877 40.000 12.12 0.00 30.90 2.97
104 105 5.123186 CCTAACAAACGGTGAATTCATAGCA 59.877 40.000 12.12 0.00 0.00 3.49
105 106 5.643379 AACAAACGGTGAATTCATAGCAT 57.357 34.783 12.12 0.00 0.00 3.79
106 107 4.985413 ACAAACGGTGAATTCATAGCATG 58.015 39.130 12.12 10.93 0.00 4.06
107 108 4.699735 ACAAACGGTGAATTCATAGCATGA 59.300 37.500 12.12 0.00 37.55 3.07
139 140 2.629617 CAACTCCTGCCAAACCAAAGAT 59.370 45.455 0.00 0.00 0.00 2.40
159 160 9.167311 CAAAGATCAATTAACCTAGCAGTAAGT 57.833 33.333 0.00 0.00 0.00 2.24
171 172 2.494870 AGCAGTAAGTACCCACGGTTAG 59.505 50.000 0.00 0.00 37.09 2.34
188 201 5.070047 ACGGTTAGCTAGTTAGTTATGCCAT 59.930 40.000 0.00 0.00 0.00 4.40
380 394 6.469410 TGAAACGAAAGCTAAGGATCCTTTA 58.531 36.000 31.45 16.04 37.47 1.85
387 405 7.698130 CGAAAGCTAAGGATCCTTTAATTGTTG 59.302 37.037 31.45 13.00 37.47 3.33
412 430 1.097232 TCACGACGTACTATGTGGGG 58.903 55.000 0.00 0.00 33.25 4.96
429 459 1.229400 GGGTGGGAGTGTGGGACTA 60.229 63.158 0.00 0.00 33.83 2.59
450 480 0.547471 TGGCTCCACTGGGAATCAGA 60.547 55.000 0.00 0.00 46.18 3.27
468 498 7.069208 GGAATCAGAATAATTGGAAGGAAGCTT 59.931 37.037 0.00 0.00 0.00 3.74
470 500 6.484288 TCAGAATAATTGGAAGGAAGCTTGA 58.516 36.000 2.10 0.00 0.00 3.02
571 607 3.868077 GCAAAGCAGAGATCGTTATCACT 59.132 43.478 0.00 0.00 33.83 3.41
572 608 4.331168 GCAAAGCAGAGATCGTTATCACTT 59.669 41.667 0.00 0.00 31.50 3.16
573 609 5.520288 GCAAAGCAGAGATCGTTATCACTTA 59.480 40.000 0.00 0.00 31.50 2.24
574 610 6.201806 GCAAAGCAGAGATCGTTATCACTTAT 59.798 38.462 0.00 0.00 31.50 1.73
575 611 7.568497 GCAAAGCAGAGATCGTTATCACTTATC 60.568 40.741 0.00 0.00 31.50 1.75
576 612 6.641169 AGCAGAGATCGTTATCACTTATCA 57.359 37.500 0.00 0.00 31.50 2.15
577 613 6.442952 AGCAGAGATCGTTATCACTTATCAC 58.557 40.000 0.00 0.00 31.50 3.06
658 694 4.166919 TGAGTAGGTCTCATCATCCTCTGA 59.833 45.833 0.00 0.00 46.77 3.27
820 868 9.770097 TTGAGCAATTTTAACATGGTCATTTAA 57.230 25.926 13.69 0.00 46.95 1.52
821 869 9.202273 TGAGCAATTTTAACATGGTCATTTAAC 57.798 29.630 10.49 0.00 44.07 2.01
822 870 9.202273 GAGCAATTTTAACATGGTCATTTAACA 57.798 29.630 0.00 0.00 40.37 2.41
823 871 9.723601 AGCAATTTTAACATGGTCATTTAACAT 57.276 25.926 0.00 0.00 0.00 2.71
824 872 9.757859 GCAATTTTAACATGGTCATTTAACATG 57.242 29.630 0.00 1.57 45.56 3.21
830 878 9.853555 TTAACATGGTCATTTAACATGATCAAC 57.146 29.630 9.87 0.00 41.81 3.18
831 879 6.866480 ACATGGTCATTTAACATGATCAACC 58.134 36.000 9.87 0.00 41.81 3.77
832 880 5.913137 TGGTCATTTAACATGATCAACCC 57.087 39.130 0.00 5.07 36.34 4.11
833 881 5.328565 TGGTCATTTAACATGATCAACCCA 58.671 37.500 0.00 6.84 36.34 4.51
834 882 5.184864 TGGTCATTTAACATGATCAACCCAC 59.815 40.000 0.00 0.00 36.34 4.61
835 883 5.418840 GGTCATTTAACATGATCAACCCACT 59.581 40.000 0.00 0.00 0.00 4.00
880 928 2.763249 CACAGAAACAAGTGGACTGC 57.237 50.000 0.00 0.00 32.67 4.40
881 929 1.334869 CACAGAAACAAGTGGACTGCC 59.665 52.381 0.00 0.00 32.67 4.85
882 930 1.212935 ACAGAAACAAGTGGACTGCCT 59.787 47.619 0.00 0.00 34.31 4.75
883 931 1.605710 CAGAAACAAGTGGACTGCCTG 59.394 52.381 0.00 0.00 34.31 4.85
884 932 0.312102 GAAACAAGTGGACTGCCTGC 59.688 55.000 0.00 0.00 34.31 4.85
885 933 1.109323 AAACAAGTGGACTGCCTGCC 61.109 55.000 0.00 0.00 34.31 4.85
886 934 1.999634 AACAAGTGGACTGCCTGCCT 62.000 55.000 0.00 0.00 34.31 4.75
887 935 1.970114 CAAGTGGACTGCCTGCCTG 60.970 63.158 0.00 0.00 34.31 4.85
888 936 3.857309 AAGTGGACTGCCTGCCTGC 62.857 63.158 0.00 0.00 34.31 4.85
967 1029 0.311790 ACACAAATCAAGCGCCAGTG 59.688 50.000 2.29 5.35 0.00 3.66
1123 1189 1.421410 GGTGAGTAATGCGCAGTCGG 61.421 60.000 16.15 0.00 35.95 4.79
1140 1206 1.343465 TCGGTCTCTTCCCTTGTTGAC 59.657 52.381 0.00 0.00 0.00 3.18
1186 1252 3.395858 CAGAATTCTGATGGACGTTGC 57.604 47.619 28.13 0.00 46.59 4.17
1265 1331 4.794439 CGGAGCATCGTGACGGCA 62.794 66.667 4.70 0.00 34.37 5.69
1375 1441 2.360165 CCATCCACTGGTACGTACTACC 59.640 54.545 24.07 12.24 45.08 3.18
1423 1489 4.783764 ATGCATGCATGATCAGTAATGG 57.216 40.909 31.74 0.00 35.03 3.16
1424 1490 2.295070 TGCATGCATGATCAGTAATGGC 59.705 45.455 30.64 10.45 0.00 4.40
1425 1491 2.295070 GCATGCATGATCAGTAATGGCA 59.705 45.455 30.64 4.63 0.00 4.92
1426 1492 3.243602 GCATGCATGATCAGTAATGGCAA 60.244 43.478 30.64 0.00 0.00 4.52
1427 1493 4.560716 GCATGCATGATCAGTAATGGCAAT 60.561 41.667 30.64 0.00 0.00 3.56
1428 1494 5.538118 CATGCATGATCAGTAATGGCAATT 58.462 37.500 22.59 0.00 0.00 2.32
1429 1495 4.939271 TGCATGATCAGTAATGGCAATTG 58.061 39.130 0.09 0.00 0.00 2.32
1430 1496 3.739300 GCATGATCAGTAATGGCAATTGC 59.261 43.478 22.47 22.47 41.14 3.56
1431 1497 4.500887 GCATGATCAGTAATGGCAATTGCT 60.501 41.667 28.42 12.82 39.07 3.91
1450 1517 2.940158 CTGATCAATGGAGGCAATGGA 58.060 47.619 0.00 0.00 0.00 3.41
1741 1812 3.246226 CACGCAGATTATTTTCCTCTCCG 59.754 47.826 0.00 0.00 0.00 4.63
1746 1844 5.419542 CAGATTATTTTCCTCTCCGTGTCA 58.580 41.667 0.00 0.00 0.00 3.58
1749 1847 7.710907 CAGATTATTTTCCTCTCCGTGTCAATA 59.289 37.037 0.00 0.00 0.00 1.90
1763 1884 4.347813 GTGTCAATACGTTGTTGCACTTT 58.652 39.130 20.27 0.00 36.69 2.66
1768 1889 6.140108 GTCAATACGTTGTTGCACTTTACAAG 59.860 38.462 1.95 0.82 35.13 3.16
1780 1935 4.032786 GCACTTTACAAGTTTTTGCACCAG 59.967 41.667 0.00 0.00 40.46 4.00
1783 1938 7.199766 CACTTTACAAGTTTTTGCACCAGATA 58.800 34.615 0.00 0.00 40.46 1.98
1784 1939 7.867403 CACTTTACAAGTTTTTGCACCAGATAT 59.133 33.333 0.00 0.00 40.46 1.63
1785 1940 8.421002 ACTTTACAAGTTTTTGCACCAGATATT 58.579 29.630 0.00 0.00 39.04 1.28
1786 1941 8.586570 TTTACAAGTTTTTGCACCAGATATTG 57.413 30.769 0.00 0.00 37.85 1.90
1787 1942 4.990426 ACAAGTTTTTGCACCAGATATTGC 59.010 37.500 0.00 0.00 37.85 3.56
1788 1943 4.870123 AGTTTTTGCACCAGATATTGCA 57.130 36.364 0.00 0.00 35.31 4.08
1789 1944 5.212532 AGTTTTTGCACCAGATATTGCAA 57.787 34.783 0.00 0.00 44.21 4.08
1790 1945 5.797051 AGTTTTTGCACCAGATATTGCAAT 58.203 33.333 17.56 17.56 45.04 3.56
1791 1946 6.232692 AGTTTTTGCACCAGATATTGCAATT 58.767 32.000 18.75 5.53 45.04 2.32
1792 1947 6.148150 AGTTTTTGCACCAGATATTGCAATTG 59.852 34.615 18.75 9.92 45.04 2.32
1793 1948 3.167921 TGCACCAGATATTGCAATTGC 57.832 42.857 23.69 23.69 42.50 3.56
1794 1949 2.121786 GCACCAGATATTGCAATTGCG 58.878 47.619 24.58 10.63 45.83 4.85
1795 1950 2.480073 GCACCAGATATTGCAATTGCGT 60.480 45.455 24.58 17.88 45.83 5.24
1796 1951 3.243035 GCACCAGATATTGCAATTGCGTA 60.243 43.478 24.58 19.35 45.83 4.42
1797 1952 4.733230 GCACCAGATATTGCAATTGCGTAA 60.733 41.667 24.58 15.07 45.83 3.18
1798 1953 5.522456 CACCAGATATTGCAATTGCGTAAT 58.478 37.500 24.58 20.43 45.83 1.89
1799 1954 6.667370 CACCAGATATTGCAATTGCGTAATA 58.333 36.000 24.58 21.74 45.83 0.98
1800 1955 6.578545 CACCAGATATTGCAATTGCGTAATAC 59.421 38.462 24.58 16.10 45.83 1.89
1801 1956 6.486657 ACCAGATATTGCAATTGCGTAATACT 59.513 34.615 24.58 17.59 45.83 2.12
1802 1957 7.017645 CCAGATATTGCAATTGCGTAATACTC 58.982 38.462 24.58 18.73 45.83 2.59
1803 1958 6.733725 CAGATATTGCAATTGCGTAATACTCG 59.266 38.462 24.58 11.43 45.83 4.18
1804 1959 3.666883 TTGCAATTGCGTAATACTCGG 57.333 42.857 24.58 0.00 45.83 4.63
1838 1993 1.128692 GCTTTCATTTCACTAGCGCGT 59.871 47.619 8.43 0.00 0.00 6.01
1846 2001 1.226295 CACTAGCGCGTGTCGATCA 60.226 57.895 8.43 0.00 41.67 2.92
1963 2118 1.136446 GTACAATTGGCGTGTGTCGTC 60.136 52.381 10.83 0.00 45.13 4.20
1964 2119 0.531974 ACAATTGGCGTGTGTCGTCT 60.532 50.000 10.83 0.00 45.15 4.18
1965 2120 0.586319 CAATTGGCGTGTGTCGTCTT 59.414 50.000 0.00 0.00 45.15 3.01
1966 2121 0.865769 AATTGGCGTGTGTCGTCTTC 59.134 50.000 0.00 0.00 45.15 2.87
1967 2122 0.033504 ATTGGCGTGTGTCGTCTTCT 59.966 50.000 0.00 0.00 45.15 2.85
1968 2123 0.669619 TTGGCGTGTGTCGTCTTCTA 59.330 50.000 0.00 0.00 45.15 2.10
1969 2124 0.885879 TGGCGTGTGTCGTCTTCTAT 59.114 50.000 0.00 0.00 45.15 1.98
1985 2140 8.191446 TCGTCTTCTATTTCTAGTTGATGAAGG 58.809 37.037 13.24 4.20 32.93 3.46
2024 2194 4.376717 GGACCGACTTAATGTGAACGTTTC 60.377 45.833 0.46 0.00 0.00 2.78
2027 2197 5.295045 ACCGACTTAATGTGAACGTTTCTTT 59.705 36.000 0.46 6.53 0.00 2.52
2041 2211 7.708752 TGAACGTTTCTTTATGGCAATTTCTTT 59.291 29.630 0.46 0.00 0.00 2.52
2087 2258 6.767423 AGCAAACAAAGGATTTACTGCAAAAT 59.233 30.769 0.00 0.00 38.07 1.82
2144 2315 6.537301 TCCAGATAACATAAGTTGCCGTAAAG 59.463 38.462 0.00 0.00 38.69 1.85
2222 2394 3.632643 TGAAATAGGCAGTGATGCTCA 57.367 42.857 0.00 0.00 34.73 4.26
2236 2408 6.099579 GTGATGCTCACACACATAAACTAG 57.900 41.667 10.30 0.00 46.22 2.57
2420 2595 0.667184 CATGCTTTCGGTTGGTTGGC 60.667 55.000 0.00 0.00 0.00 4.52
2507 2684 6.087291 CGAAATTTATACTATCACGTCGGTCC 59.913 42.308 0.00 0.00 0.00 4.46
2628 2805 5.982356 TGTGAGATCCTTCTTTACTCATGG 58.018 41.667 0.00 0.00 39.27 3.66
2727 3832 6.926272 AGCCTTAAGAAATTCAGATACTAGCG 59.074 38.462 3.36 0.00 0.00 4.26
2740 3849 2.588027 ACTAGCGCCTTTCTAGCTTC 57.412 50.000 2.29 0.00 41.88 3.86
2745 3854 1.131315 GCGCCTTTCTAGCTTCCAAAG 59.869 52.381 0.00 0.00 0.00 2.77
2802 3911 6.859017 TCATCATGAAAATGTTCCATGTCTG 58.141 36.000 0.00 0.00 32.28 3.51
2809 3918 0.539438 TGTTCCATGTCTGGTTGGCC 60.539 55.000 0.00 0.00 43.61 5.36
2833 3942 7.162082 CCGAGCCTCTTATACATTATTTCCTT 58.838 38.462 0.00 0.00 0.00 3.36
2869 3978 5.831702 AAGAGAGAAAGCATGCATAAAGG 57.168 39.130 21.98 0.00 0.00 3.11
2899 4008 6.951256 TCAACATGTTCTAATGTTCTCTCG 57.049 37.500 8.48 0.00 45.47 4.04
2977 4088 5.614324 AGTGCTGGCTATATCTTGTTGTA 57.386 39.130 0.00 0.00 0.00 2.41
2982 4093 6.828273 TGCTGGCTATATCTTGTTGTAATGTT 59.172 34.615 0.00 0.00 0.00 2.71
3013 4124 6.414732 AGCAAGTCTAAATAGCCAACATGTA 58.585 36.000 0.00 0.00 0.00 2.29
3035 4450 3.430042 TTGCATTCAAGAAGAGCTCCT 57.570 42.857 10.93 0.00 0.00 3.69
3042 4457 4.696479 TCAAGAAGAGCTCCTTGAAAGT 57.304 40.909 24.58 0.00 43.84 2.66
3043 4458 5.041191 TCAAGAAGAGCTCCTTGAAAGTT 57.959 39.130 24.58 6.62 43.84 2.66
3083 4498 7.164826 GCATAGATTCGCAATAAACAAAGTCTG 59.835 37.037 0.00 0.00 0.00 3.51
3133 4552 9.806203 CTGTCATTTATTTCATAATTTGGCTGA 57.194 29.630 0.00 0.00 0.00 4.26
3228 4648 0.107703 TGTGGTACAGCATGCTAGCC 60.108 55.000 22.19 21.34 41.80 3.93
3233 4653 2.033801 GGTACAGCATGCTAGCCAATTG 59.966 50.000 22.19 8.91 42.53 2.32
3279 4704 4.256110 TCAGCTGTTCAATATGTGGAGTG 58.744 43.478 14.67 0.00 0.00 3.51
3290 4715 0.830444 TGTGGAGTGGTACGCCTTCT 60.830 55.000 3.50 0.00 38.97 2.85
3383 4979 7.549839 AGAGCTAGATAGATAGTACAGTACCG 58.450 42.308 7.13 0.00 0.00 4.02
3391 4987 5.648572 AGATAGTACAGTACCGTTTTCTGC 58.351 41.667 7.13 0.00 33.12 4.26
3413 5009 4.543692 CAACTAATAATCTGGCTGCATGC 58.456 43.478 11.82 11.82 41.94 4.06
3925 5934 1.519676 CACGGTCACCACGTTCACA 60.520 57.895 0.00 0.00 43.58 3.58
4634 6646 6.347160 GCCAATTTGCTGAAGAAATCAAAGTC 60.347 38.462 0.00 0.00 37.67 3.01
4840 8362 3.937778 TTCCTGCATCATGAGATCCAA 57.062 42.857 0.09 0.00 30.20 3.53
4903 8647 1.155889 TCATTTACCACTGCACTGCG 58.844 50.000 0.00 0.00 0.00 5.18
4973 8717 2.807967 TGTCGGTCTGCAAAAAGATCTG 59.192 45.455 0.00 0.00 0.00 2.90
5039 8786 6.484643 TCTGATAAAAGCACAGATCATTAGGC 59.515 38.462 0.00 0.00 36.04 3.93
5312 9059 2.421399 GGCCTCCAGATTTGCCTGC 61.421 63.158 0.00 0.00 40.77 4.85
5383 9131 2.852714 TACTCCCTCCGTCCCATAAA 57.147 50.000 0.00 0.00 0.00 1.40
5471 9219 9.624697 TGTATATGTCAAGAAAGAAATTTGCAC 57.375 29.630 0.00 0.00 0.00 4.57
5499 9248 0.180406 CCTAGTTCCCATCCAACCCG 59.820 60.000 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 8.424274 TGTACATCAGCAAATACTTAGTGATG 57.576 34.615 8.26 8.26 44.44 3.07
6 7 9.618890 AATGTACATCAGCAAATACTTAGTGAT 57.381 29.630 9.23 0.00 0.00 3.06
7 8 9.448438 AAATGTACATCAGCAAATACTTAGTGA 57.552 29.630 9.23 0.00 0.00 3.41
16 17 9.884636 TGTACTACTAAATGTACATCAGCAAAT 57.115 29.630 9.23 0.00 42.49 2.32
17 18 9.713713 TTGTACTACTAAATGTACATCAGCAAA 57.286 29.630 9.23 0.00 45.35 3.68
18 19 9.366216 CTTGTACTACTAAATGTACATCAGCAA 57.634 33.333 9.23 7.69 45.35 3.91
19 20 7.491372 GCTTGTACTACTAAATGTACATCAGCA 59.509 37.037 9.23 0.00 44.46 4.41
20 21 7.491372 TGCTTGTACTACTAAATGTACATCAGC 59.509 37.037 9.23 16.51 45.35 4.26
21 22 8.926715 TGCTTGTACTACTAAATGTACATCAG 57.073 34.615 9.23 11.77 45.35 2.90
22 23 9.146984 GTTGCTTGTACTACTAAATGTACATCA 57.853 33.333 9.23 0.00 45.35 3.07
23 24 9.146984 TGTTGCTTGTACTACTAAATGTACATC 57.853 33.333 9.23 0.00 45.35 3.06
24 25 9.151471 CTGTTGCTTGTACTACTAAATGTACAT 57.849 33.333 1.41 1.41 45.35 2.29
25 26 8.361889 TCTGTTGCTTGTACTACTAAATGTACA 58.638 33.333 0.00 0.00 44.68 2.90
26 27 8.752766 TCTGTTGCTTGTACTACTAAATGTAC 57.247 34.615 0.00 0.00 39.37 2.90
27 28 9.419297 CTTCTGTTGCTTGTACTACTAAATGTA 57.581 33.333 0.00 0.00 0.00 2.29
28 29 8.148351 TCTTCTGTTGCTTGTACTACTAAATGT 58.852 33.333 0.00 0.00 0.00 2.71
29 30 8.534333 TCTTCTGTTGCTTGTACTACTAAATG 57.466 34.615 0.00 0.00 0.00 2.32
30 31 8.989980 GTTCTTCTGTTGCTTGTACTACTAAAT 58.010 33.333 0.00 0.00 0.00 1.40
31 32 7.982919 TGTTCTTCTGTTGCTTGTACTACTAAA 59.017 33.333 0.00 0.00 0.00 1.85
32 33 7.437267 GTGTTCTTCTGTTGCTTGTACTACTAA 59.563 37.037 0.00 0.00 0.00 2.24
33 34 6.921857 GTGTTCTTCTGTTGCTTGTACTACTA 59.078 38.462 0.00 0.00 0.00 1.82
34 35 5.753921 GTGTTCTTCTGTTGCTTGTACTACT 59.246 40.000 0.00 0.00 0.00 2.57
35 36 5.050295 GGTGTTCTTCTGTTGCTTGTACTAC 60.050 44.000 0.00 0.00 0.00 2.73
36 37 5.054477 GGTGTTCTTCTGTTGCTTGTACTA 58.946 41.667 0.00 0.00 0.00 1.82
37 38 3.877508 GGTGTTCTTCTGTTGCTTGTACT 59.122 43.478 0.00 0.00 0.00 2.73
38 39 3.625764 TGGTGTTCTTCTGTTGCTTGTAC 59.374 43.478 0.00 0.00 0.00 2.90
39 40 3.879998 TGGTGTTCTTCTGTTGCTTGTA 58.120 40.909 0.00 0.00 0.00 2.41
40 41 2.722094 TGGTGTTCTTCTGTTGCTTGT 58.278 42.857 0.00 0.00 0.00 3.16
41 42 3.567164 AGATGGTGTTCTTCTGTTGCTTG 59.433 43.478 0.00 0.00 0.00 4.01
42 43 3.825328 AGATGGTGTTCTTCTGTTGCTT 58.175 40.909 0.00 0.00 0.00 3.91
43 44 3.498774 AGATGGTGTTCTTCTGTTGCT 57.501 42.857 0.00 0.00 0.00 3.91
44 45 4.569943 TCTAGATGGTGTTCTTCTGTTGC 58.430 43.478 0.00 0.00 32.85 4.17
45 46 6.169094 ACATCTAGATGGTGTTCTTCTGTTG 58.831 40.000 31.19 7.38 42.91 3.33
46 47 6.365970 ACATCTAGATGGTGTTCTTCTGTT 57.634 37.500 31.19 7.60 42.91 3.16
47 48 6.437477 TGTACATCTAGATGGTGTTCTTCTGT 59.563 38.462 31.19 13.57 42.91 3.41
48 49 6.867550 TGTACATCTAGATGGTGTTCTTCTG 58.132 40.000 31.19 8.58 42.91 3.02
49 50 7.667575 ATGTACATCTAGATGGTGTTCTTCT 57.332 36.000 31.19 13.27 42.91 2.85
50 51 8.723942 AAATGTACATCTAGATGGTGTTCTTC 57.276 34.615 31.19 11.69 42.91 2.87
51 52 9.520515 AAAAATGTACATCTAGATGGTGTTCTT 57.479 29.630 31.19 16.96 42.91 2.52
74 75 7.769220 TGAATTCACCGTTTGTTAGGTAAAAA 58.231 30.769 3.38 0.00 39.00 1.94
75 76 7.330900 TGAATTCACCGTTTGTTAGGTAAAA 57.669 32.000 3.38 0.00 39.00 1.52
76 77 6.939132 TGAATTCACCGTTTGTTAGGTAAA 57.061 33.333 3.38 0.00 39.00 2.01
77 78 7.148373 GCTATGAATTCACCGTTTGTTAGGTAA 60.148 37.037 11.07 0.00 39.00 2.85
78 79 6.314400 GCTATGAATTCACCGTTTGTTAGGTA 59.686 38.462 11.07 0.00 39.00 3.08
79 80 5.123344 GCTATGAATTCACCGTTTGTTAGGT 59.877 40.000 11.07 0.00 42.34 3.08
80 81 5.123186 TGCTATGAATTCACCGTTTGTTAGG 59.877 40.000 11.07 0.00 0.00 2.69
81 82 6.176975 TGCTATGAATTCACCGTTTGTTAG 57.823 37.500 11.07 7.14 0.00 2.34
82 83 6.372937 TCATGCTATGAATTCACCGTTTGTTA 59.627 34.615 11.07 0.00 36.11 2.41
83 84 5.182950 TCATGCTATGAATTCACCGTTTGTT 59.817 36.000 11.07 0.00 36.11 2.83
84 85 4.699735 TCATGCTATGAATTCACCGTTTGT 59.300 37.500 11.07 0.00 36.11 2.83
85 86 5.233957 TCATGCTATGAATTCACCGTTTG 57.766 39.130 11.07 6.73 36.11 2.93
86 87 5.895636 TTCATGCTATGAATTCACCGTTT 57.104 34.783 11.07 0.00 43.84 3.60
96 97 4.586421 TGTTGGGTTTGTTCATGCTATGAA 59.414 37.500 7.27 7.27 46.30 2.57
97 98 4.148079 TGTTGGGTTTGTTCATGCTATGA 58.852 39.130 0.00 0.00 37.55 2.15
98 99 4.517952 TGTTGGGTTTGTTCATGCTATG 57.482 40.909 0.00 0.00 0.00 2.23
99 100 4.588528 AGTTGTTGGGTTTGTTCATGCTAT 59.411 37.500 0.00 0.00 0.00 2.97
100 101 3.957497 AGTTGTTGGGTTTGTTCATGCTA 59.043 39.130 0.00 0.00 0.00 3.49
101 102 2.765699 AGTTGTTGGGTTTGTTCATGCT 59.234 40.909 0.00 0.00 0.00 3.79
102 103 3.123050 GAGTTGTTGGGTTTGTTCATGC 58.877 45.455 0.00 0.00 0.00 4.06
103 104 3.384467 AGGAGTTGTTGGGTTTGTTCATG 59.616 43.478 0.00 0.00 0.00 3.07
104 105 3.384467 CAGGAGTTGTTGGGTTTGTTCAT 59.616 43.478 0.00 0.00 0.00 2.57
105 106 2.757868 CAGGAGTTGTTGGGTTTGTTCA 59.242 45.455 0.00 0.00 0.00 3.18
106 107 2.481276 GCAGGAGTTGTTGGGTTTGTTC 60.481 50.000 0.00 0.00 0.00 3.18
107 108 1.480545 GCAGGAGTTGTTGGGTTTGTT 59.519 47.619 0.00 0.00 0.00 2.83
108 109 1.111277 GCAGGAGTTGTTGGGTTTGT 58.889 50.000 0.00 0.00 0.00 2.83
109 110 0.389025 GGCAGGAGTTGTTGGGTTTG 59.611 55.000 0.00 0.00 0.00 2.93
110 111 0.032615 TGGCAGGAGTTGTTGGGTTT 60.033 50.000 0.00 0.00 0.00 3.27
139 140 6.441284 TGGGTACTTACTGCTAGGTTAATTGA 59.559 38.462 0.00 0.00 0.00 2.57
159 160 3.968265 ACTAACTAGCTAACCGTGGGTA 58.032 45.455 0.00 0.00 33.12 3.69
171 172 7.259290 TGCTTTTATGGCATAACTAACTAGC 57.741 36.000 19.11 18.07 34.56 3.42
240 254 7.781548 TGTCTGTTCTACACCTTTACTTTTC 57.218 36.000 0.00 0.00 0.00 2.29
281 295 2.508407 TTTCCGAATCCAAGGCCCCC 62.508 60.000 0.00 0.00 0.00 5.40
380 394 7.591006 AGTACGTCGTGATTAATCAACAATT 57.409 32.000 19.55 7.40 38.75 2.32
387 405 5.628193 CCCACATAGTACGTCGTGATTAATC 59.372 44.000 8.47 8.60 0.00 1.75
392 410 1.679680 CCCCACATAGTACGTCGTGAT 59.320 52.381 8.47 0.00 0.00 3.06
395 413 0.323725 ACCCCCACATAGTACGTCGT 60.324 55.000 2.21 2.21 0.00 4.34
412 430 0.544595 ACTAGTCCCACACTCCCACC 60.545 60.000 0.00 0.00 36.43 4.61
450 480 5.774690 TGTGTCAAGCTTCCTTCCAATTATT 59.225 36.000 0.00 0.00 0.00 1.40
495 525 3.262915 AGCTAGAGGTTGCTTTCATCTGT 59.737 43.478 0.00 0.00 35.86 3.41
571 607 5.988287 TGAGTGCCATATTGACTGTGATAA 58.012 37.500 0.00 0.00 0.00 1.75
572 608 5.612725 TGAGTGCCATATTGACTGTGATA 57.387 39.130 0.00 0.00 0.00 2.15
573 609 4.492494 TGAGTGCCATATTGACTGTGAT 57.508 40.909 0.00 0.00 0.00 3.06
574 610 3.979101 TGAGTGCCATATTGACTGTGA 57.021 42.857 0.00 0.00 0.00 3.58
575 611 3.246936 CGATGAGTGCCATATTGACTGTG 59.753 47.826 0.00 0.00 35.17 3.66
576 612 3.461061 CGATGAGTGCCATATTGACTGT 58.539 45.455 0.00 0.00 35.17 3.55
577 613 2.222678 GCGATGAGTGCCATATTGACTG 59.777 50.000 0.00 0.00 35.17 3.51
658 694 4.985538 TCCATCACAAGTTAAGCCTTTCT 58.014 39.130 0.00 0.00 0.00 2.52
830 878 2.224042 GGAAAGCAAAAGAACCAGTGGG 60.224 50.000 15.21 0.00 41.29 4.61
831 879 2.430332 TGGAAAGCAAAAGAACCAGTGG 59.570 45.455 7.91 7.91 0.00 4.00
832 880 3.799281 TGGAAAGCAAAAGAACCAGTG 57.201 42.857 0.00 0.00 0.00 3.66
833 881 5.357742 AATTGGAAAGCAAAAGAACCAGT 57.642 34.783 0.00 0.00 0.00 4.00
834 882 4.751600 GGAATTGGAAAGCAAAAGAACCAG 59.248 41.667 0.00 0.00 0.00 4.00
835 883 4.163078 TGGAATTGGAAAGCAAAAGAACCA 59.837 37.500 0.00 0.00 0.00 3.67
840 888 4.273235 GTGGTTGGAATTGGAAAGCAAAAG 59.727 41.667 0.00 0.00 33.53 2.27
889 937 1.495579 ATATAGGGGCAGGCAGGCAG 61.496 60.000 5.69 0.00 46.44 4.85
890 938 0.178876 TATATAGGGGCAGGCAGGCA 60.179 55.000 5.69 0.00 46.44 4.75
891 939 0.991920 TTATATAGGGGCAGGCAGGC 59.008 55.000 0.00 0.00 43.27 4.85
892 940 1.561542 CCTTATATAGGGGCAGGCAGG 59.438 57.143 2.89 0.00 40.67 4.85
938 1000 3.187637 GCTTGATTTGTGTGCAATGCAAT 59.812 39.130 10.44 0.00 41.47 3.56
939 1001 2.544686 GCTTGATTTGTGTGCAATGCAA 59.455 40.909 10.44 0.00 41.47 4.08
940 1002 2.136728 GCTTGATTTGTGTGCAATGCA 58.863 42.857 2.72 2.72 34.18 3.96
941 1003 1.125384 CGCTTGATTTGTGTGCAATGC 59.875 47.619 0.00 0.00 34.18 3.56
942 1004 1.125384 GCGCTTGATTTGTGTGCAATG 59.875 47.619 0.00 0.00 37.20 2.82
967 1029 3.092780 GCTCTGCTCCCTCCTGCTC 62.093 68.421 0.00 0.00 0.00 4.26
1080 1142 1.080093 CTCGTGGCGTTGCTCCTTA 60.080 57.895 0.00 0.00 0.00 2.69
1123 1189 1.149148 GCGTCAACAAGGGAAGAGAC 58.851 55.000 0.00 0.00 0.00 3.36
1140 1206 1.600957 CCAGCCATTAGTGAATCTGCG 59.399 52.381 0.00 0.00 0.00 5.18
1197 1263 5.423290 CCTCCTGGATCTGCATACATACATA 59.577 44.000 0.00 0.00 34.57 2.29
1198 1264 4.224594 CCTCCTGGATCTGCATACATACAT 59.775 45.833 0.00 0.00 34.57 2.29
1199 1265 3.580022 CCTCCTGGATCTGCATACATACA 59.420 47.826 0.00 0.00 34.57 2.29
1200 1266 3.618507 GCCTCCTGGATCTGCATACATAC 60.619 52.174 0.00 0.00 34.57 2.39
1201 1267 2.568956 GCCTCCTGGATCTGCATACATA 59.431 50.000 0.00 0.00 34.57 2.29
1202 1268 1.350351 GCCTCCTGGATCTGCATACAT 59.650 52.381 0.00 0.00 34.57 2.29
1296 1362 2.654877 GGAGTCGCCCTCGTTCAA 59.345 61.111 0.00 0.00 41.46 2.69
1409 1475 4.982295 CAGCAATTGCCATTACTGATCATG 59.018 41.667 26.45 9.70 43.38 3.07
1410 1476 4.891168 TCAGCAATTGCCATTACTGATCAT 59.109 37.500 26.45 0.16 37.72 2.45
1411 1477 4.271661 TCAGCAATTGCCATTACTGATCA 58.728 39.130 26.45 0.00 37.72 2.92
1412 1478 4.906065 TCAGCAATTGCCATTACTGATC 57.094 40.909 26.45 0.00 37.72 2.92
1414 1480 4.271661 TGATCAGCAATTGCCATTACTGA 58.728 39.130 26.45 21.14 43.88 3.41
1417 1483 4.748102 CCATTGATCAGCAATTGCCATTAC 59.252 41.667 26.45 14.49 44.68 1.89
1418 1484 4.650131 TCCATTGATCAGCAATTGCCATTA 59.350 37.500 26.45 12.84 44.68 1.90
1419 1485 3.452990 TCCATTGATCAGCAATTGCCATT 59.547 39.130 26.45 11.38 44.68 3.16
1420 1486 3.035363 TCCATTGATCAGCAATTGCCAT 58.965 40.909 26.45 18.40 44.68 4.40
1421 1487 2.429250 CTCCATTGATCAGCAATTGCCA 59.571 45.455 26.45 14.43 44.68 4.92
1422 1488 2.223971 CCTCCATTGATCAGCAATTGCC 60.224 50.000 26.45 11.88 44.68 4.52
1423 1489 2.802057 GCCTCCATTGATCAGCAATTGC 60.802 50.000 23.05 23.05 44.68 3.56
1424 1490 2.429250 TGCCTCCATTGATCAGCAATTG 59.571 45.455 0.00 0.00 44.68 2.32
1425 1491 2.742348 TGCCTCCATTGATCAGCAATT 58.258 42.857 2.83 0.00 44.68 2.32
1427 1493 2.219080 TTGCCTCCATTGATCAGCAA 57.781 45.000 12.30 12.30 41.53 3.91
1428 1494 2.028876 CATTGCCTCCATTGATCAGCA 58.971 47.619 1.25 1.25 0.00 4.41
1429 1495 1.340248 CCATTGCCTCCATTGATCAGC 59.660 52.381 0.00 0.00 0.00 4.26
1430 1496 2.940158 TCCATTGCCTCCATTGATCAG 58.060 47.619 0.00 0.00 0.00 2.90
1431 1497 3.227614 CATCCATTGCCTCCATTGATCA 58.772 45.455 0.00 0.00 0.00 2.92
1432 1498 2.561419 CCATCCATTGCCTCCATTGATC 59.439 50.000 0.00 0.00 0.00 2.92
1433 1499 2.605257 CCATCCATTGCCTCCATTGAT 58.395 47.619 0.00 0.00 0.00 2.57
1434 1500 2.030571 GCCATCCATTGCCTCCATTGA 61.031 52.381 0.00 0.00 0.00 2.57
1435 1501 0.391597 GCCATCCATTGCCTCCATTG 59.608 55.000 0.00 0.00 0.00 2.82
1741 1812 3.602390 AGTGCAACAACGTATTGACAC 57.398 42.857 20.15 20.15 41.43 3.67
1763 1884 6.155827 GCAATATCTGGTGCAAAAACTTGTA 58.844 36.000 0.00 0.00 40.58 2.41
1780 1935 6.015504 CCGAGTATTACGCAATTGCAATATC 58.984 40.000 28.77 19.59 42.21 1.63
1783 1938 3.874543 TCCGAGTATTACGCAATTGCAAT 59.125 39.130 28.77 22.36 42.21 3.56
1784 1939 3.263261 TCCGAGTATTACGCAATTGCAA 58.737 40.909 28.77 17.33 42.21 4.08
1785 1940 2.894902 TCCGAGTATTACGCAATTGCA 58.105 42.857 28.77 11.27 42.21 4.08
1786 1941 3.604392 GTTCCGAGTATTACGCAATTGC 58.396 45.455 20.76 20.76 37.78 3.56
1787 1942 3.302221 CCGTTCCGAGTATTACGCAATTG 60.302 47.826 0.00 0.00 32.97 2.32
1788 1943 2.861935 CCGTTCCGAGTATTACGCAATT 59.138 45.455 0.00 0.00 32.97 2.32
1789 1944 2.099592 TCCGTTCCGAGTATTACGCAAT 59.900 45.455 0.00 0.00 32.97 3.56
1790 1945 1.472082 TCCGTTCCGAGTATTACGCAA 59.528 47.619 0.00 0.00 32.97 4.85
1791 1946 1.064505 CTCCGTTCCGAGTATTACGCA 59.935 52.381 0.00 0.00 32.97 5.24
1792 1947 1.598924 CCTCCGTTCCGAGTATTACGC 60.599 57.143 0.00 0.00 32.97 4.42
1793 1948 1.002033 CCCTCCGTTCCGAGTATTACG 60.002 57.143 0.00 0.00 0.00 3.18
1794 1949 2.292845 CTCCCTCCGTTCCGAGTATTAC 59.707 54.545 0.00 0.00 0.00 1.89
1795 1950 2.092212 ACTCCCTCCGTTCCGAGTATTA 60.092 50.000 0.00 0.00 33.87 0.98
1796 1951 1.341778 ACTCCCTCCGTTCCGAGTATT 60.342 52.381 0.00 0.00 33.87 1.89
1797 1952 0.258194 ACTCCCTCCGTTCCGAGTAT 59.742 55.000 0.00 0.00 33.87 2.12
1798 1953 0.911769 TACTCCCTCCGTTCCGAGTA 59.088 55.000 0.00 0.00 36.91 2.59
1799 1954 0.394080 CTACTCCCTCCGTTCCGAGT 60.394 60.000 0.00 0.00 38.97 4.18
1800 1955 1.726533 GCTACTCCCTCCGTTCCGAG 61.727 65.000 0.00 0.00 0.00 4.63
1801 1956 1.751927 GCTACTCCCTCCGTTCCGA 60.752 63.158 0.00 0.00 0.00 4.55
1802 1957 1.321074 AAGCTACTCCCTCCGTTCCG 61.321 60.000 0.00 0.00 0.00 4.30
1803 1958 0.903236 AAAGCTACTCCCTCCGTTCC 59.097 55.000 0.00 0.00 0.00 3.62
1804 1959 1.549170 TGAAAGCTACTCCCTCCGTTC 59.451 52.381 0.00 0.00 0.00 3.95
1809 1964 4.837972 AGTGAAATGAAAGCTACTCCCTC 58.162 43.478 0.00 0.00 0.00 4.30
1838 1993 1.248101 TGCCGAGGACTTGATCGACA 61.248 55.000 0.00 0.00 41.40 4.35
1846 2001 2.743183 GCTATCATTGTGCCGAGGACTT 60.743 50.000 0.00 0.00 0.00 3.01
1872 2027 0.845102 AGGTCCTGGTGTAAAGGGGG 60.845 60.000 0.00 0.00 35.35 5.40
1873 2028 1.838077 CTAGGTCCTGGTGTAAAGGGG 59.162 57.143 0.00 0.00 35.35 4.79
1963 2118 9.255304 GTAGCCTTCATCAACTAGAAATAGAAG 57.745 37.037 0.00 4.57 0.00 2.85
1964 2119 8.982723 AGTAGCCTTCATCAACTAGAAATAGAA 58.017 33.333 0.00 0.00 0.00 2.10
1965 2120 8.417106 CAGTAGCCTTCATCAACTAGAAATAGA 58.583 37.037 0.00 0.00 0.00 1.98
1966 2121 8.200792 ACAGTAGCCTTCATCAACTAGAAATAG 58.799 37.037 0.00 0.00 0.00 1.73
1967 2122 7.981789 CACAGTAGCCTTCATCAACTAGAAATA 59.018 37.037 0.00 0.00 0.00 1.40
1968 2123 6.820656 CACAGTAGCCTTCATCAACTAGAAAT 59.179 38.462 0.00 0.00 0.00 2.17
1969 2124 6.166279 CACAGTAGCCTTCATCAACTAGAAA 58.834 40.000 0.00 0.00 0.00 2.52
1985 2140 1.373570 GTCCTTCATGCCACAGTAGC 58.626 55.000 0.00 0.00 0.00 3.58
2027 2197 9.814899 CCATGTGTTTATAAAGAAATTGCCATA 57.185 29.630 0.00 0.00 0.00 2.74
2041 2211 7.637631 TGCTAGAATTTGCCATGTGTTTATA 57.362 32.000 0.00 0.00 0.00 0.98
2045 2215 4.870123 TTGCTAGAATTTGCCATGTGTT 57.130 36.364 0.00 0.00 0.00 3.32
2087 2258 5.713792 TTCCTTCAAGTGAACACAACAAA 57.286 34.783 7.68 0.00 0.00 2.83
2122 2293 6.537660 GTCCTTTACGGCAACTTATGTTATCT 59.462 38.462 0.00 0.00 34.60 1.98
2144 2315 5.057149 AGGAGCATGATAAAACATACGTCC 58.943 41.667 0.00 0.00 0.00 4.79
2197 2369 4.666237 GCATCACTGCCTATTTCAAGAAC 58.334 43.478 0.00 0.00 42.88 3.01
2260 2432 8.327271 TCAAGAGTCCACTACTACTACTTGTAT 58.673 37.037 0.00 0.00 39.07 2.29
2280 2455 9.837525 CTAAATTCCTTTCTGTCATTTCAAGAG 57.162 33.333 0.00 0.00 0.00 2.85
2381 2556 1.684450 GCATGCATGGGAATGATGACA 59.316 47.619 27.34 0.00 30.90 3.58
2507 2684 2.286713 TGCATGGTTTTCGTTCGTCTTG 60.287 45.455 0.00 0.00 0.00 3.02
2556 2733 3.578716 GCTCCATGGTAGTAGCTATCCAA 59.421 47.826 12.58 3.60 33.55 3.53
2557 2734 3.165875 GCTCCATGGTAGTAGCTATCCA 58.834 50.000 12.58 14.49 32.18 3.41
2727 3832 6.543831 TGAATATCTTTGGAAGCTAGAAAGGC 59.456 38.462 10.53 0.00 0.00 4.35
2740 3849 8.742777 TCCTTTGATTTGTCTGAATATCTTTGG 58.257 33.333 0.00 0.00 0.00 3.28
2745 3854 8.566260 CATCCTCCTTTGATTTGTCTGAATATC 58.434 37.037 0.00 0.00 0.00 1.63
2809 3918 9.706691 TTAAGGAAATAATGTATAAGAGGCTCG 57.293 33.333 9.22 0.00 0.00 5.03
2833 3942 9.793259 TGCTTTCTCTCTTTAGAATTCCTTTTA 57.207 29.630 0.65 0.00 35.48 1.52
2869 3978 5.772521 ACATTAGAACATGTTGAAACTGGC 58.227 37.500 17.58 0.00 33.29 4.85
2899 4008 9.256477 AGATTATTTTTCTTTCAAACCCGTTTC 57.744 29.630 0.00 0.00 0.00 2.78
2982 4093 9.326413 GTTGGCTATTTAGACTTGCTAGAAATA 57.674 33.333 1.04 1.86 30.79 1.40
2987 4098 6.540189 ACATGTTGGCTATTTAGACTTGCTAG 59.460 38.462 0.00 0.00 30.79 3.42
2991 4102 9.507280 CAATTACATGTTGGCTATTTAGACTTG 57.493 33.333 2.30 0.00 30.79 3.16
2992 4103 8.190784 GCAATTACATGTTGGCTATTTAGACTT 58.809 33.333 2.30 0.00 30.79 3.01
2994 4105 7.479980 TGCAATTACATGTTGGCTATTTAGAC 58.520 34.615 2.30 0.00 0.00 2.59
2995 4106 7.637631 TGCAATTACATGTTGGCTATTTAGA 57.362 32.000 2.30 0.00 0.00 2.10
2998 4109 7.329499 TGAATGCAATTACATGTTGGCTATTT 58.671 30.769 2.30 0.00 36.07 1.40
3013 4124 4.342359 AGGAGCTCTTCTTGAATGCAATT 58.658 39.130 14.64 0.00 40.93 2.32
3035 4450 5.066634 TGCAATTACGGACTCAAACTTTCAA 59.933 36.000 0.00 0.00 0.00 2.69
3042 4457 6.019075 CGAATCTATGCAATTACGGACTCAAA 60.019 38.462 0.00 0.00 0.00 2.69
3043 4458 5.462068 CGAATCTATGCAATTACGGACTCAA 59.538 40.000 0.00 0.00 0.00 3.02
3123 4542 7.521910 GCAACAACCAAAATAATCAGCCAAATT 60.522 33.333 0.00 0.00 0.00 1.82
3133 4552 4.505922 CACACACGCAACAACCAAAATAAT 59.494 37.500 0.00 0.00 0.00 1.28
3140 4559 3.057547 GCCACACACGCAACAACCA 62.058 57.895 0.00 0.00 0.00 3.67
3242 4662 6.208599 TGAACAGCTGAAAATACTAAAAGGGG 59.791 38.462 23.35 0.00 0.00 4.79
3252 4677 7.611467 ACTCCACATATTGAACAGCTGAAAATA 59.389 33.333 23.35 19.12 0.00 1.40
3279 4704 5.464030 TTCATATAGGAAGAAGGCGTACC 57.536 43.478 0.00 0.00 0.00 3.34
3383 4979 6.749118 CAGCCAGATTATTAGTTGCAGAAAAC 59.251 38.462 0.00 0.00 0.00 2.43
3391 4987 4.543692 GCATGCAGCCAGATTATTAGTTG 58.456 43.478 14.21 0.00 37.23 3.16
3889 5889 1.740296 GGCCGTGTCATTGTACGCT 60.740 57.895 9.57 0.00 38.87 5.07
3925 5934 4.626081 AGGTTGCGCAGGCTCGTT 62.626 61.111 11.31 0.00 40.82 3.85
4087 6099 2.359404 GAGACGGTGGAGGGGAGA 59.641 66.667 0.00 0.00 0.00 3.71
4448 6460 0.033796 ATGACAGCCCACCCATTCAG 60.034 55.000 0.00 0.00 0.00 3.02
4651 6671 6.096846 ACATTGCCCCAAATAATCAGTAGAAC 59.903 38.462 0.00 0.00 0.00 3.01
4840 8362 7.010552 GCACTAAGATTGATTTCAGTGTACGAT 59.989 37.037 0.00 0.00 36.59 3.73
4903 8647 2.032924 GCTGGTGGTTGTGTACTTCAAC 59.967 50.000 18.94 18.94 42.76 3.18
4973 8717 1.069358 CTAGCCAAGTAGTAGCCAGGC 59.931 57.143 1.84 1.84 42.31 4.85
5059 8806 4.910195 TGGAGTTATGTTCAATGCAGTCT 58.090 39.130 0.00 0.00 0.00 3.24
5312 9059 6.265422 AGAAGATTTTTACCCCTGAACTGTTG 59.735 38.462 0.00 0.00 0.00 3.33
5471 9219 3.954258 GGATGGGAACTAGGAAATTGTGG 59.046 47.826 0.00 0.00 0.00 4.17
5499 9248 7.703197 GCTTTACAAGAGGTGAGTAGAATAGAC 59.297 40.741 0.00 0.00 0.00 2.59
5524 9273 3.058639 GCGGTAAGATCTTTCATGGATGC 60.059 47.826 14.36 3.68 0.00 3.91


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.